Early detection of SARS-CoV-2 variants using genomic surveillance: insights from aircraft wastewater and nasal swabs at Kigali International Airport, Rwanda

Abstract

Objectives: The growing threat of emerging infectious diseases necessitates proactive genomic surveillance, particularly, in regions with limited resources and low levels of existing reporting. This study highlights the implementation of a comprehensive genomic surveillance program at the Kigali International Airport and explores the utility of a dual-sample strategy leveraging environmental aircraft wastewater and pooled nasal swab sample types for comprehensive detection and characterization of SARS-CoV-2 lineages being imported into Rwanda.

Methods: Using a combined pooled nasal swab and aircraft wastewater sampling approach resulted in complementary insights in terms of geographic coverage, positivity, and variant characterization.

Results: Mutational profiling in source pooled nasal swabs and aircraft wastewater sample data revealed dynamic shifts in mutation prevalence that corresponded with global patterns. Emerging variant JN.1 was detected early in nasal swab data, demonstrating the power of using genomic surveillance as an early warning system.

Conclusions: These results support the feasibility of pathogen surveillance in high-traffic settings and may help drive interest in expanding programs to include pathogens beyond SARS-CoV-2.

Keywords: SARS-Cov2; Surveillance; Traveler genomics.

Figure 1

Overview of sample processing workflow. For pooled samples (a), travelers volunteer to collect two nasal swabs at the airport; swabs are grouped in pools (5-10 swabs/pool) and sent to the laboratory. Wastewater samples are collected by aircraft ground handlers from the aircraft lavatories (a). Samples are then transported (b) in temperature-stabilized boxes and shipped overnight to a central laboratory. Once samples have reached the laboratory, nucleic acids are extracted (c). All samples are then tested for SARS-CoV-2 using reverse transcription–qPCR (d). Samples positive for PCR then undergo tiled amplicon sequencing (e). Sequencing data are then analyzed to determine the presence of viral variants (f). qPCR, quantitative polymerase chain reaction.

Figure 2

Summary of polymerase chain reaction positivity and sample collection for pooled nasal swabs (a and c) and wastewater (b and d). Bar charts (left) show the number of samples collected by week and whether the sample was positive or negative for SARS-CoV-2 by quantitative reverse transcription–polymerase chain reaction. The maps (right) summarize sample collection breadth of geographic coverage based on flight origin country.

Figure 3

Relationship between flight duration and SARS-CoV-2 detection in wastewater (a) and pooled nasal swabs (b) at Kigali International Airport. (a) In aircraft wastewater, a near-perfect break point was observed at 6 hours (360 minutes), with the percentage of positive samples increased with longer flight durations. (b) For pooled nasal swab samples (b), the number of positive samples increased as flight duration extended. Overall, the detection rate in nasal swabs was lower than aircraft wastewater samples.

Figure 4

Diversity and abundance of SARS-CoV-2 variants detected by collection date through pooled nasal swab (a) and aircraft wastewater (b) sequencing from July 2023 to May 2024.

Figure 5

Timeline of collection dates of samples sequenced by this program alongside their first detections worldwide, in Africa, and in countries neighboring Rwanda. DRC = Democratic Republic of Congo; Global = first location a respective variant was detected worldwide; VOI = World Health Organization designated variant of interest; VUM = World Health Organization–designated variant under monitoring; WW = wastewater sample.